def upload_to_ndex(self):
"""Upload the assembled model as CX to NDEx"""
assembled_stmts = self.run_assembly()
cxa = CxAssembler(assembled_stmts, network_name=self.name)
cxa.make_model()
cx_str = cxa.print_cx()
ndex_client.update_network(cx_str, self.ndex_network)
def assemble_cx(stmts, name):
ca = CxAssembler()
ca.network_name = name
ca.add_statements(stmts)
ca.make_model()
cx_str = ca.print_cx()
return cx_str
def assemble_cx(stmts, name):
ca = CxAssembler()
ca.network_name = name
ca.add_statements(stmts)
ca.make_model()
cx_str = ca.print_cx()
return cx_str
def update_to_ndex(self):
"""Update assembled model as CX on NDEx, updates existing network."""
if not self.assembled_stmts:
self.run_assembly()
cxa = CxAssembler(self.assembled_stmts, network_name=self.name)
cxa.make_model()
cx_str = cxa.print_cx()
ndex_client.update_network(cx_str, self.ndex_network)
def test_cited():
cxa = CxAssembler()
cxa.add_statements([st_cited])
cxa.make_model()
assert len(cxa.cx['citations']) == 1
assert len(cxa.cx['edgeCitations']) == 1
citation = cxa.cx['citations'][0]
assert citation.get('dc:identifier') == 'pmid:12345'
cid = citation.get('@id')
assert cxa.cx['edgeCitations'][0]['citations'][0] == cid
print(cxa.print_cx())
def test_cited():
cxa = CxAssembler()
cxa.add_statements([st_cited])
cxa.make_model()
assert len(cxa.cx['citations']) == 1
assert len(cxa.cx['edgeCitations']) == 1
citation = cxa.cx['citations'][0]
assert citation.get('dc:identifier') == 'pmid:12345'
cid = citation.get('@id')
assert cxa.cx['edgeCitations'][0]['citations'][0] == cid
print(cxa.print_cx())